SGCG
Basic information
Region (hg38): 13:23180979-23325162
Previous symbols: [ "DMDA1", "MAM", "LGMD2C" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy type 2C (Strong), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy type 2C (Supportive), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
- autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Muscular dystrophy, limb-girdle, limb-girdle, autosomal recessive, 5 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal | 1303286; 7481775; 8923014; 8968757; 10507732; 10720277; 16832103; 18285821 |
ClinVar
This is a list of variants' phenotypes submitted to
- Autosomal recessive limb-girdle muscular dystrophy type 2C (34 variants)
- not provided (8 variants)
- Abnormality of the musculature (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCG gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 97 | 104 | ||||
missense | 127 | 136 | ||||
nonsense | 12 | 19 | ||||
start loss | 0 | |||||
frameshift | 22 | 21 | 43 | |||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 18 | 23 | ||||
splice region | 1 | 9 | 17 | 3 | 30 | |
non coding | 84 | 40 | 132 | |||
Total | 34 | 54 | 144 | 184 | 43 |
Highest pathogenic variant AF is 0.000158
Variants in SGCG
This is a list of pathogenic ClinVar variants found in the SGCG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
13-23180988-G-A | Limb-girdle muscular dystrophy, recessive • Sarcoglycanopathy | Benign/Likely benign (Nov 19, 2019) | ||
13-23181070-T-C | Sarcoglycanopathy • Limb-girdle muscular dystrophy, recessive • not specified • SGCG-related disorder | Conflicting classifications of pathogenicity (Sep 01, 2024) | ||
13-23181080-G-A | Autosomal recessive limb-girdle muscular dystrophy type 2C | Conflicting classifications of pathogenicity (Mar 14, 2024) | ||
13-23181294-T-C | Likely benign (May 24, 2021) | |||
13-23203416-A-T | Likely benign (Sep 04, 2018) | |||
13-23203451-T-G | Likely benign (Sep 05, 2018) | |||
13-23203521-A-C | Likely benign (Sep 05, 2018) | |||
13-23203603-C-T | Likely benign (Sep 05, 2018) | |||
13-23203687-C-T | not specified | Conflicting classifications of pathogenicity (Feb 04, 2016) | ||
13-23203692-C-T | Autosomal recessive limb-girdle muscular dystrophy type 2C • Autosomal recessive limb-girdle muscular dystrophy | Likely benign (Jan 08, 2025) | ||
13-23203699-T-C | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Aug 03, 2022) | ||
13-23203701-C-T | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Jul 15, 2022) | ||
13-23203702-G-A | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Oct 13, 2022) | ||
13-23203704-G-T | Autosomal recessive limb-girdle muscular dystrophy type 2C | Likely pathogenic (Oct 24, 2023) | ||
13-23203706-G-T | not specified | Uncertain significance (May 17, 2024) | ||
13-23203711-A-G | Autosomal recessive limb-girdle muscular dystrophy type 2C • Sarcoglycanopathy | Uncertain significance (Mar 05, 2023) | ||
13-23203716-A-G | Autosomal recessive limb-girdle muscular dystrophy type 2C • Inborn genetic diseases | Uncertain significance (Sep 01, 2022) | ||
13-23203721-C-T | Autosomal recessive limb-girdle muscular dystrophy type 2C | Likely benign (Feb 01, 2022) | ||
13-23203728-G-A | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Apr 02, 2019) | ||
13-23203732-T-A | Inborn genetic diseases | Uncertain significance (Aug 28, 2023) | ||
13-23203736-C-T | Autosomal recessive limb-girdle muscular dystrophy type 2C | Likely benign (Jan 27, 2024) | ||
13-23203738-T-C | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Jun 02, 2021) | ||
13-23203739-A-G | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Aug 05, 2021) | ||
13-23203740-G-C | Autosomal recessive limb-girdle muscular dystrophy type 2C | Uncertain significance (Mar 08, 2022) | ||
13-23203751-G-A | Autosomal recessive limb-girdle muscular dystrophy type 2C | Likely benign (Sep 19, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SGCG | protein_coding | protein_coding | ENST00000218867 | 7 | 144214 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000482 | 0.876 | 125705 | 0 | 43 | 125748 | 0.000171 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.134 | 168 | 163 | 1.03 | 0.00000874 | 1881 |
Missense in Polyphen | 64 | 65.214 | 0.98139 | 773 | ||
Synonymous | -1.14 | 73 | 61.6 | 1.18 | 0.00000359 | 562 |
Loss of Function | 1.44 | 9 | 15.0 | 0.600 | 7.03e-7 | 180 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000667 | 0.000666 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000193 | 0.000193 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000989 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.;
- Pathway
- Dilated cardiomyopathy (DCM) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy
(Consensus)
Recessive Scores
- pRec
- 0.363
Intolerance Scores
- loftool
- 0.314
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.77
Haploinsufficiency Scores
- pHI
- 0.111
- hipred
- N
- hipred_score
- 0.390
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0893
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sgcg
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;
Gene ontology
- Biological process
- muscle organ development;cardiac muscle tissue development;heart contraction
- Cellular component
- nucleoplasm;cytoplasm;cytoskeleton;plasma membrane;sarcoglycan complex;integral component of membrane;sarcolemma
- Molecular function
- protein binding